Queen Mary died in 1558 and was succeeded by Elizabeth, daughter of Anne Boleyn, the executed second wife of Henry VIII. Elizabeth re-established Protestantism as the State Church. She had both Catholic and Protestant suitors but by not marrying a Protestant she encouraged her Catholic subjects to remain loyal and kept Phillip II of Spain from taking direct military action against her for several years.

In Ireland Munster, Connacht and Leinster were subdivided for administrative purposes into the counties that exist today. Munster had been difficult to overcome as religion had been a rallying point for the anti English forces. An uprising in Munster in 1579 was vigorously put down and the lands of the rebel lords were sized and planted with English colonists. In 1580 Walter Raleigh was in charge at Smerwick in County Kerry when 700 Spanish and Italians who had been sent by Philip of Spain and Pope Gregory XIII to help the Irish were massacred. In return Raleigh was given 4,000 acres of Irish land.>

There was also an uprising in Leinster led by Viscount Baltinglass and Fiach McHugh O'Byrne. Though they defeated the government forces at the Battle of Glenmalure in 1580, the uprising ended in defeat. The taking of Connacht was comparatively easy, but in Ulster the chieftains, knowing what had happened in the other provinces and with first hand experience of the violence and duplicity of the English, stood their ground against Anglicisation.